{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:36:19Z","timestamp":1773279379479,"version":"3.50.1"},"reference-count":24,"publisher":"SAGE Publications","issue":"10","license":[{"start":{"date-parts":[[2024,10,1]],"date-time":"2024-10-01T00:00:00Z","timestamp":1727740800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Journal of Computational Biology"],"published-print":{"date-parts":[[2024,10,1]]},"abstract":"<jats:p>\n                    An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, sequence repeats, regions with a particular epigenetic state, and copy number variants. A common task is to compare two annotations to determine if one is enriched or depleted in the regions covered by the other. We study the problem of assigning statistical significance to such a comparison based on a null model representing random unrelated annotations. To incorporate more background information into such analyses, we propose a new null model based on a Markov chain that differentiates among several genomic contexts. These contexts can capture various confounding factors, such as GC content or assembly gaps. We then develop a new algorithm for estimating\n                    <jats:italic toggle=\"yes\">p<\/jats:italic>\n                    -values by computing the exact expectation and variance of the test statistic and then estimating the\n                    <jats:italic toggle=\"yes\">p<\/jats:italic>\n                    -value using a normal approximation. Compared to the previous algorithm by Gafurov et al., the new algorithm provides three advances: (1) the running time is improved from quadratic to linear or quasi-linear, (2) the algorithm can handle two different test statistics, and (3) the algorithm can handle both simple and context-dependent Markov chain null models. We demonstrate the efficiency and accuracy of our algorithm on synthetic and real data sets, including the recent human telomere-to-telomere assembly. In particular, our algorithm computed\n                    <jats:italic toggle=\"yes\">p<\/jats:italic>\n                    -values for 450 pairs of human genome annotations using 24 threads in under three hours. Moreover, the use of genomic contexts to correct for GC bias resulted in the reversal of some previously published findings.\n                  <\/jats:p>","DOI":"10.1089\/cmb.2024.0667","type":"journal-article","created":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T04:38:16Z","timestamp":1728448696000},"page":"946-964","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Fast Context-Aware Analysis of Genome Annotation Colocalization"],"prefix":"10.1177","volume":"31","author":[{"given":"Askar","family":"Gafurov","sequence":"first","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia."},{"name":"LIRMM, University of Montpellier, Montpellier, France."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom\u00e1\u0161","family":"Vina\u0158","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Medvedev","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA."},{"name":"Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA."},{"name":"Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9483-1766","authenticated-orcid":false,"given":"Bro\u0147a","family":"Brejov\u00e1","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2024,10,30]]},"reference":[{"key":"e_1_3_4_2_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1997.0951"},{"key":"e_1_3_4_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2438-1"},{"key":"e_1_3_4_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw169"},{"key":"e_1_3_4_5_1","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492"},{"key":"e_1_3_4_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac255"},{"key":"e_1_3_4_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv562"},{"key":"e_1_3_4_8_1","doi-asserted-by":"publisher","DOI":"10.2217\/epi.13.32"},{"key":"e_1_3_4_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj5089"},{"key":"e_1_3_4_10_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.seminhematol.2008.04.003"},{"key":"e_1_3_4_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.05.042"},{"key":"e_1_3_4_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt343"},{"key":"e_1_3_4_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty835"},{"key":"e_1_3_4_14_1","volume-title":"Probabilistic Graphical Models: Principles and Techniques","author":"Koller D","year":"2009","unstructured":"Koller D, , Friedman N. Probabilistic Graphical Models: Principles and Techniques. MIT Press; 2009."},{"key":"e_1_3_4_15_1","doi-asserted-by":"publisher","DOI":"10.1137\/1122001"},{"key":"e_1_3_4_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1072"},{"key":"e_1_3_4_17_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj6987"},{"key":"e_1_3_4_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_3_4_19_1","doi-asserted-by":"publisher","DOI":"10.1214\/11-PS182"},{"key":"e_1_3_4_20_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-12-r121"},{"key":"e_1_3_4_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2019.05.006"},{"key":"e_1_3_4_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv612"},{"key":"e_1_3_4_23_1","doi-asserted-by":"publisher","DOI":"10.4300\/JGME-D-12-00156.1"},{"key":"e_1_3_4_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3871"},{"key":"e_1_3_4_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5573107"}],"container-title":["Journal of Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/cmb.2024.0667","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/cmb.2024.0667","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/cmb.2024.0667","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T11:00:38Z","timestamp":1773226838000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1089\/cmb.2024.0667"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,1]]},"references-count":24,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2024,10,1]]}},"alternative-id":["10.1089\/cmb.2024.0667"],"URL":"https:\/\/doi.org\/10.1089\/cmb.2024.0667","relation":{},"ISSN":["1066-5277","1557-8666"],"issn-type":[{"value":"1066-5277","type":"print"},{"value":"1557-8666","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,1]]}}}